MOL204 - Aim and content
The aim for this course is to give students knowledge of and competence in use of bioinformatical methods central to conduction of molecular biological research projects. The course has emphasis on bioinformatics related to exploration of proteins and includes analyses of sequences, database searches, sequence comparison, visualization and analysis of protein structures, and introduction to phylogenetic analyses. The students will get an introduction to the theoretical foundations for a few key methods. The course will also give an introduction to analysis of DNA sequences, genes and genomes, gene expression and systems biology. Through practical exercises, the course aims to give students a basic competences in the use of bioinformatical tools. The course emphasizes the the learning of bioinformatical tools in light of the student's knowledge of molecular biology.
On completion of the course the student should have the following learning outcomes defined in terms of knowledge, skills and general competence:
- The student can explain which type of data is available from the most common protein sequence and structure databases (UniProt, GenBank, Protein Data Bank, CATH).
- The candidate can explain the theories underlying the most common methods for sequence searches and sequence alignments, and in particular knows the principle and main steps for pairwise and multiple sequence alignments;
- The student can explain and is able to apply the main steps of dynamic programing for/to simple alignments of short sequences;
- The student can list methods to uncover structure-function relationship in proteins and knows their underlying principles;
- The student can explain the principles of computational methods for the prediction of secondary structure elements from protein sequence, prediction and modeling of three-dimensional protein structures (homology modeling, threading and ab initio methods).
The student is able to:
- select and apply the most appropriate bioinformatics sequence or structure database to retrieve or search data given a specific question in molecular biology;
- select and apply the most appropriate method for aligning sequences, visualizing and analyzing protein structures, predicting secondary structure elements and modeling protein structures from sequence.
- The student is able to reflect using its knowledge and skills in bioinformatics so as to decide whether a given molecular biology problem could benefit from a bioinformatics approach, and which methods to use.
- Using their theoretical knowledge about the most commonly used bioinformatics methods, the student is able, if encountering a new online tool, to get a general understanding of its underlying principle]